De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification.
De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification.
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DOI：
10.1186/1471-2164-15-453
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发表时间：
2014-06-09
期刊：
影响因子：
4.4
通讯作者：
Skøt L
中科院分区：
文献类型：
--
作者：
Yates SA;Swain MT;Hegarty MJ;Chernukin I;Lowe M;Allison GG;Ruttink T;Abberton MT;Jenkins G;Skøt L
红三叶（Trifolium pratense L.）是一种多用途的饲料作物豆科植物，它可以耐受各种土壤，适合于冬季饲料和放牧的青贮生产。它是温带畜牧业中最重要的饲用豆科植物之一。它的有益属性包括固氮、改良土壤和提供富含蛋白质的动物饲料的能力。然而，它是一种短命的多年生植物，可提供两三年的良好生物量产量。因此，改良的持久性是一个主要的育种目标。较好的水分胁迫耐受性是影响红三叶持续性的关键因素之一，但目前对红三叶如何耐受水分胁迫知之甚少。来自全同胞作图家族的植物用于干旱实验，其中生长速率和相对含水量（RWC）鉴定了两个池的10株植物，所述两个池的10株植物在其耐旱性方面形成对比。测量了关键代谢物，并对四个散装样品进行了RNA-Seq分析：干旱前后采样的两个池。使用大规模平行测序来分析批量RNA样品。进行基于RNA-Seq数据的从头转录组重建，产生45181个重叠群，代表"转录物标签"。这些转录物标签用基因本体（GO）术语注释。表达分析的最引人注目的结果之一是干旱敏感植物的特征在于在干旱后具有比耐受植物大约两倍的差异表达转录物标签的数量。这种差异在大多数主要的GO术语中都很明显。在干旱发生之前，敏感的植物过度表达了一些与衰老相关的基因。此外，浓度的三种代谢产物，特别是松醇，但也脯氨酸和苹果酸在干旱胁迫后的叶片增加。从干旱和非干旱植物的叶材料中从头组装红三叶草转录组为基因鉴定、单核苷酸多态性（SNP）和短序列重复（SSR）提供了丰富的来源。比较池和处理之间的基因表达水平，确定候选基因，以进一步分析红三叶草耐旱性的遗传基础。本文的在线版本（doi：10.1186/1471 - 2164 - 15 - 453）包含补充材料，可供授权用户使用。
Red clover (Trifolium pratense L.) is a versatile forage crop legume, which can tolerate a variety of soils and is suitable for silage production for winter feed and for grazing. It is one of the most important forage legumes in temperate livestock agriculture. Its beneficial attributes include ability to fix nitrogen, improve soil and provide protein rich animal feed. It is however, a short-lived perennial providing good biomass yield for two or three years. Improved persistency is thus a major breeding target. Better water-stress tolerance is one of the key factors influencing persistency, but little is known about how red clover tolerates water stress. Plants from a full sib mapping family were used in a drought experiment, in which the growth rate and relative water content (RWC) identified two pools of ten plants contrasting in their tolerance to drought. Key metabolites were measured and RNA-Seq analysis was carried out on four bulked samples: the two pools sampled before and after drought. Massively parallel sequencing was used to analyse the bulked RNA samples. A de novo transcriptome reconstruction based on the RNA-Seq data was made, resulting in 45181 contigs, representing ‘transcript tags’. These transcript tags were annotated with gene ontology (GO) terms. One of the most striking results from the expression analysis was that the drought sensitive plants were characterised by having approximately twice the number of differentially expressed transcript tags than the tolerant plants after drought. This difference was evident in most of the major GO terms. Before onset of drought the sensitive plants overexpressed a number of genes annotated as senescence-related. Furthermore, the concentration of three metabolites, particularly pinitol, but also proline and malate increased in leaves after drought stress. This de novo assembly of a red clover transcriptome from leaf material of droughted and non-droughted plants provides a rich source for gene identification, single nucleotide polymorphisms (SNP) and short sequence repeats (SSR). Comparison of gene expression levels between pools and treatments identified candidate genes for further analysis of the genetic basis of drought tolerance in red clover. The online version of this article (doi:10.1186/1471-2164-15-453) contains supplementary material, which is available to authorized users.
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影响因子：
4.4
作者：
Aprile A;Mastrangelo AM;De Leonardis AM;Galiba G;Roncaglia E;Ferrari F;De Bellis L;Turchi L;Giuliano G;Cattivelli L
通讯作者：
Cattivelli L
影响因子：
4.4
作者：
Mizrachi E;Hefer CA;Ranik M;Joubert F;Myburg AA
通讯作者：
Myburg AA
影响因子：
6.9
作者：
MINCHIN, FR;MINGUEZ, MI;SKOT, L
通讯作者：
SKOT, L
影响因子：
3.8
作者：
FORD, CW
通讯作者：
FORD, CW
影响因子：
4.2
作者：
Flexas, J;Medrano, H
通讯作者：
Medrano, H